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Adr1 and Cat8 mediate coactivator recruitment and chromatin remodeling at glucose-regulated genes.

Biddick RK, Law GL, Young ET - PLoS ONE (2008)

Bottom Line: We determined the individual contributions of Cat8 and Adr1 on the expression of a cohort of glucose-repressed genes and found three broad categories: genes that need both activators for full derepression, genes that rely mostly on Cat8 and genes that require only Adr1.These promoter-specific contributions are also apparent in the chromatin remodeling that accompanies derepression: ADH2 requires both Adr1 and Cat8, whereas, at FBP1, significant remodeling occurs with Cat8 alone.Thus, at many of the glucose-repressed genes, Cat8 and Adr1 appear to have interchangeable roles and promoter architecture may dictate the roles of these activators.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry, University of Washington, Seattle, Washington, United States of America.

ABSTRACT

Background: Adr1 and Cat8 co-regulate numerous glucose-repressed genes in S. cerevisiae, presenting a unique opportunity to explore their individual roles in coactivator recruitment, chromatin remodeling, and transcription.

Methodology/principal findings: We determined the individual contributions of Cat8 and Adr1 on the expression of a cohort of glucose-repressed genes and found three broad categories: genes that need both activators for full derepression, genes that rely mostly on Cat8 and genes that require only Adr1. Through combined expression and recruitment data, along with analysis of chromatin remodeling at two of these genes, ADH2 and FBP1, we clarified how these activators achieve this wide range of co-regulation. We find that Adr1 and Cat8 are not intrinsically different in their abilities to recruit coactivators but rather, promoter context appears to dictate which activator is responsible for recruitment to specific genes. These promoter-specific contributions are also apparent in the chromatin remodeling that accompanies derepression: ADH2 requires both Adr1 and Cat8, whereas, at FBP1, significant remodeling occurs with Cat8 alone. Although over-expression of Adr1 can compensate for loss of Cat8 at many genes in terms of both activation and chromatin remodeling, this over-expression cannot complement all of the cat8Delta phenotypes.

Conclusions/significance: Thus, at many of the glucose-repressed genes, Cat8 and Adr1 appear to have interchangeable roles and promoter architecture may dictate the roles of these activators.

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Related in: MedlinePlus

Differential roles for Adr1 and Cat8 in chromatin remodeling at ADH2 and FBP1.NuSA results are displayed as the amount of relative protection, after normalization to the well-positioned nucleosome at CEN3. The position of each amplicon (referenced to the middle of each amplicon) within the promoter is shown on the x-axis, with approximate location of nucleosomes shown. (A) and (C) are the results at ADH2, (B) and (D) are at FBP1. (A) and (B) compare NuSA results of Δadr1 (pink) and Δcat8 (green) in derepressed conditions to a wildtype strain either in repressed (dark blue) or derepressed (light blue) conditions. (C) and (D) compare NuSA results between over-expression of Adr1 with (red) or without Cat8 (blue) in derepressed conditions.
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pone-0001436-g002: Differential roles for Adr1 and Cat8 in chromatin remodeling at ADH2 and FBP1.NuSA results are displayed as the amount of relative protection, after normalization to the well-positioned nucleosome at CEN3. The position of each amplicon (referenced to the middle of each amplicon) within the promoter is shown on the x-axis, with approximate location of nucleosomes shown. (A) and (C) are the results at ADH2, (B) and (D) are at FBP1. (A) and (B) compare NuSA results of Δadr1 (pink) and Δcat8 (green) in derepressed conditions to a wildtype strain either in repressed (dark blue) or derepressed (light blue) conditions. (C) and (D) compare NuSA results between over-expression of Adr1 with (red) or without Cat8 (blue) in derepressed conditions.

Mentions: Differential recruitment of known coactivators seems unable to explain the dependence of gene expression on both Adr1 and Cat8. Specific recruitment of unknown coactivators may explain this apparent conundrum. Another possibility is that a step in gene activation requires the simultaneous participation of both Adr1 and Cat8. Previous studies in our lab and others show that specific changes in promoter architecture at both ADH2 and FBP1 occur upon derepression and these changes do not occur in a adr1cat8 double mutant [24], (Infante, unpublished). To determine whether or not the two activators have redundant roles in terms of chromatin structure, we used a nucleosome scanning assay, or NuSA, to measure both nucleosome occupancy and location within the promoter in different yeast strains [25]. Figure 2A shows chromatin remodeling at the ADH2 promoter in a wild-type strain upon derepression: there is a reduction in protection at all 3 nucleosome positions as predicted [25]. These changes depended on both Adr1 and Cat8, as loss of either one of these activators in derepressing conditions abolished this remodeling. These findings agree with the expression data, in that both activators are required for a substantial increase in expression upon derepression (Table 1). The NuSA at the FBP1 promoter with a wild-type strain showed changes in chromatin structure upon derepression–a major reduction of protection at N-1 and N-2 and a shift in position of N-2 (Fig. 2B) ([25], Infante unpublished data). However, in this case, differences were seen between the two deletion strains. In the Δadr1 strain, a significant amount of remodeling occurred. There was a major reduction of occupancy at N-1, occupancy at N-2 was reduced to approximately 50% of repressed levels and the position of N-2 shifted downstream as in wildtype under derepressing conditions. Remodeling in the absence of Cat8, however, was reduced. Some reduction in the N-1 occupancy occurred but less than in the Δadr1 strain, and the occupancy of N-2 did not change, other than a partial shift in the position. Again the FBP1 chromatin remodeling agrees with the expression data, in that there is a role for both Adr1 and Cat8, albeit an unequal one.


Adr1 and Cat8 mediate coactivator recruitment and chromatin remodeling at glucose-regulated genes.

Biddick RK, Law GL, Young ET - PLoS ONE (2008)

Differential roles for Adr1 and Cat8 in chromatin remodeling at ADH2 and FBP1.NuSA results are displayed as the amount of relative protection, after normalization to the well-positioned nucleosome at CEN3. The position of each amplicon (referenced to the middle of each amplicon) within the promoter is shown on the x-axis, with approximate location of nucleosomes shown. (A) and (C) are the results at ADH2, (B) and (D) are at FBP1. (A) and (B) compare NuSA results of Δadr1 (pink) and Δcat8 (green) in derepressed conditions to a wildtype strain either in repressed (dark blue) or derepressed (light blue) conditions. (C) and (D) compare NuSA results between over-expression of Adr1 with (red) or without Cat8 (blue) in derepressed conditions.
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC2175534&req=5

pone-0001436-g002: Differential roles for Adr1 and Cat8 in chromatin remodeling at ADH2 and FBP1.NuSA results are displayed as the amount of relative protection, after normalization to the well-positioned nucleosome at CEN3. The position of each amplicon (referenced to the middle of each amplicon) within the promoter is shown on the x-axis, with approximate location of nucleosomes shown. (A) and (C) are the results at ADH2, (B) and (D) are at FBP1. (A) and (B) compare NuSA results of Δadr1 (pink) and Δcat8 (green) in derepressed conditions to a wildtype strain either in repressed (dark blue) or derepressed (light blue) conditions. (C) and (D) compare NuSA results between over-expression of Adr1 with (red) or without Cat8 (blue) in derepressed conditions.
Mentions: Differential recruitment of known coactivators seems unable to explain the dependence of gene expression on both Adr1 and Cat8. Specific recruitment of unknown coactivators may explain this apparent conundrum. Another possibility is that a step in gene activation requires the simultaneous participation of both Adr1 and Cat8. Previous studies in our lab and others show that specific changes in promoter architecture at both ADH2 and FBP1 occur upon derepression and these changes do not occur in a adr1cat8 double mutant [24], (Infante, unpublished). To determine whether or not the two activators have redundant roles in terms of chromatin structure, we used a nucleosome scanning assay, or NuSA, to measure both nucleosome occupancy and location within the promoter in different yeast strains [25]. Figure 2A shows chromatin remodeling at the ADH2 promoter in a wild-type strain upon derepression: there is a reduction in protection at all 3 nucleosome positions as predicted [25]. These changes depended on both Adr1 and Cat8, as loss of either one of these activators in derepressing conditions abolished this remodeling. These findings agree with the expression data, in that both activators are required for a substantial increase in expression upon derepression (Table 1). The NuSA at the FBP1 promoter with a wild-type strain showed changes in chromatin structure upon derepression–a major reduction of protection at N-1 and N-2 and a shift in position of N-2 (Fig. 2B) ([25], Infante unpublished data). However, in this case, differences were seen between the two deletion strains. In the Δadr1 strain, a significant amount of remodeling occurred. There was a major reduction of occupancy at N-1, occupancy at N-2 was reduced to approximately 50% of repressed levels and the position of N-2 shifted downstream as in wildtype under derepressing conditions. Remodeling in the absence of Cat8, however, was reduced. Some reduction in the N-1 occupancy occurred but less than in the Δadr1 strain, and the occupancy of N-2 did not change, other than a partial shift in the position. Again the FBP1 chromatin remodeling agrees with the expression data, in that there is a role for both Adr1 and Cat8, albeit an unequal one.

Bottom Line: We determined the individual contributions of Cat8 and Adr1 on the expression of a cohort of glucose-repressed genes and found three broad categories: genes that need both activators for full derepression, genes that rely mostly on Cat8 and genes that require only Adr1.These promoter-specific contributions are also apparent in the chromatin remodeling that accompanies derepression: ADH2 requires both Adr1 and Cat8, whereas, at FBP1, significant remodeling occurs with Cat8 alone.Thus, at many of the glucose-repressed genes, Cat8 and Adr1 appear to have interchangeable roles and promoter architecture may dictate the roles of these activators.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry, University of Washington, Seattle, Washington, United States of America.

ABSTRACT

Background: Adr1 and Cat8 co-regulate numerous glucose-repressed genes in S. cerevisiae, presenting a unique opportunity to explore their individual roles in coactivator recruitment, chromatin remodeling, and transcription.

Methodology/principal findings: We determined the individual contributions of Cat8 and Adr1 on the expression of a cohort of glucose-repressed genes and found three broad categories: genes that need both activators for full derepression, genes that rely mostly on Cat8 and genes that require only Adr1. Through combined expression and recruitment data, along with analysis of chromatin remodeling at two of these genes, ADH2 and FBP1, we clarified how these activators achieve this wide range of co-regulation. We find that Adr1 and Cat8 are not intrinsically different in their abilities to recruit coactivators but rather, promoter context appears to dictate which activator is responsible for recruitment to specific genes. These promoter-specific contributions are also apparent in the chromatin remodeling that accompanies derepression: ADH2 requires both Adr1 and Cat8, whereas, at FBP1, significant remodeling occurs with Cat8 alone. Although over-expression of Adr1 can compensate for loss of Cat8 at many genes in terms of both activation and chromatin remodeling, this over-expression cannot complement all of the cat8Delta phenotypes.

Conclusions/significance: Thus, at many of the glucose-repressed genes, Cat8 and Adr1 appear to have interchangeable roles and promoter architecture may dictate the roles of these activators.

Show MeSH
Related in: MedlinePlus